Research workbench
Crystal structure of zikv NS5 methyltransferase in complex with GTP and sah
Analyse Crystal structure of zikv NS5 methyltransferase in complex with GTP and sah in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GP1
- Type
- protein
- Length
- 783 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA-directed RNA polymerase NS5
- UniProt
- H9A910
- Ligands
- GTA, SAH, NI, SO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase NS5 | protein | 262 | 37% helix, 17% strand | H9A910 |
| B | RNA-directed RNA polymerase NS5 | protein | 260 | 37% helix, 16% strand | H9A910 |
| C | RNA-directed RNA polymerase NS5 | protein | 261 | 36% helix, 17% strand | H9A910 |
Ligands and binding sites
- GTA · P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate · ligand · 3 copies · chains A, B, C
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, B, C
- NI · Nickel (II) ion · metal · chains C
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.76 | 0.78 | 104 | SAH |
| 2 | 675 | 0.68 | 0.77 | 46 | empty |
| 3 | 487 | 0.65 | 0.77 | 52 | SO4, SAH |
| 4 | 455 | 0.63 | 0.77 | 43 | SO4, SAH |
| 5 | 289 | 0.61 | 0.79 | 34 | SO4 |
Interfaces
3 interfaces between chains.
- B–C · 677 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 464 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 27 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5GP1 · Crystal structure of ZIKV NS5 Methyltransferase in complex with GTP and SAH · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt H9A910
- Elsewhere: RCSB PDB 5GP1 · PDBe 5GP1 · UniProt H9A910
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